The state-of-the-art method generating potential functions used in molecular dynamics is based on machine learning with neural networks, which is critical for molecular dynamics simulation. This method provides an efficient way for fitting multi-variable nonlinear functions, attracting extensive attention in recent years. Generally, the quality of potentials fitted by neural networks is heavily affected by training datasets and the training process and could be ensured by comprehensively verificating the model accuracy. In this study, we obtained the neural network potential of face-centered cubic (FCC) Cu with the most accurate and adequate training datasets from first-principle calculations and the training process performed by Deep Potential Molecular Dynamics (DeePMD). This potential could not only succeed in reproductions of the variety of properties of Cu at 0 K, but also have a good performance at finite temperatures, such as predicting elastic constants and the melting point. Moreover, our potential has a better generalization capacity to predict the grain boundary energy without including extra datasets about grain boundary structures. These results support the applicability of the method under more practical conditions.
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http://dx.doi.org/10.1039/d2cp02758e | DOI Listing |
Background: The increased incidence of Alzheimer's disease (AD) rate represent an unmet medical need and thus critical for the development of novel molecular therapeutics. Recent work focusing on patients with apoE4 alleles has highlighted the association of brain cholesterol dysregulation with elevated pathological burden and neurodegeneration. These studies have highlighted the importance of the nuclear receptor Liver X receptor (LXR) for developing AD therapies.
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View Article and Find Full Text PDFJ Phys Chem A
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Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada.
We report a new NMR method for treating two-site chemical exchange involving half-integer quadrupolar nuclei in a solution. The new method was experimentally verified with extensive Na ( = 3/2), K ( = 3/2), and Rb ( = 3/2) NMR results from alkali metal ions (Na, K, and Rb) in a solution over a wide range of molecular tumbling conditions. In the fast-motion limit, all allowed single-quantum NMR transitions for a particular quadrupolar nucleus are degenerate giving rise to one Lorentzian signal.
View Article and Find Full Text PDFJ Chem Inf Model
January 2025
Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany.
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View Article and Find Full Text PDFInt J Biol Sci
January 2025
Department of Basic & Translational Sciences, School of Dental Medicine, University of Pennsylvania, USA.
Inositol polyphosphate-5-phosphatase E (INPP5E) is a 5-phosphatase critically involved in diverse physiological processes, including embryonic development, neurological function, immune regulation, hemopoietic cell dynamics, and macrophage proliferation, differentiation, and phagocytosis. Mutations in cause Joubert and Meckel-Gruber syndromes in humans; these are characterized by brain malformations, microphthalmia, situs inversus, skeletal abnormalities, and polydactyly. Recent studies have demonstrated the key role of INPP5E in governing intracellular processes like endocytosis, exocytosis, vesicular trafficking, and membrane dynamics.
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